"why does he hate her?"
he doesn't, he never did, what he hated, and fought against, was the system that made possible that orphans became child soldiers for her father, like, how can something be so obviously in your face and somehow people still miss it
It is precisely because his justification makes no sense for his actions. He acts like he hates her, he tortures her, he covets her and wants her at the palm of his hand. He hates that his fantasies about love and company he worked so hard for couldn't become reality because of his political and ethical interests, and justifies his cruelty with what you said ignoring that he's already gathered enough power and has killed the main players of the system. In other words, his actions now have little to do with the system itself. You're over simplifying his character yet claim that the ones that pick on the obvious contradictions are the ones missing the point.
I feel like this sort of emotional contradiction is kinda a common trope tbh and honestly not that uncommon irl. You don't just lose feelings because you justify them away. That in itself can cause one to lash out, even more so when the person is mentally not stable. He was telling himself consciously or subconsciously that she was unchanging in her ignorant innocence and was unaffected by what was going on. He was telling himself this so he didnt have to address the same contradiction you point out. And because, to him, she was unchanging, he didn't have to care for her actively and could lash out at her
None of thats great ofc but I really don't think his character is that big of an evil
kinda obsessed on how they're on the same length of toxicity with each other